Contacts of the helix formed by residues 74 - 83 (chain G) in PDB entry 4XLN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 74 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65G PHE 4.2 5.4 - - - +
67G THR* 4.9 12.3 - - + +
68G ILE* 6.0 1.8 - - - +
72G LYS 3.7 3.0 + - - -
73G GLU* 1.3 78.1 - - - +
75G VAL* 1.3 63.2 + - - +
76G VAL* 3.1 7.6 + - - +
77G GLU* 3.0 27.4 + - - +
78G ILE* 3.0 20.9 + - - +
627I ARG* 2.7 21.6 + - - +
628I TYR* 2.7 35.6 + - + -
640I ARG* 2.5 33.6 + - - -
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G ILE* 5.9 3.4 - - + -
61G VAL* 3.9 21.5 - - + -
63G HIS 3.4 23.6 - - - +
64G GLU* 3.3 16.5 + - - +
65G PHE 3.9 5.1 + - - +
66G SER 3.1 27.8 - - - +
68G ILE* 4.9 6.9 - - + +
74G ASP* 1.3 74.5 + - - +
76G VAL* 1.3 58.7 + - - +
78G ILE* 2.9 14.3 + - - +
79G ILE* 2.9 41.2 + - + +
165G ILE* 4.4 4.0 - - + -
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Residues in contact with VAL 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G GLU* 3.0 43.7 + - + +
65G PHE* 5.6 3.4 - - + -
74G ASP* 3.1 14.6 + - - +
75G VAL* 1.3 78.4 - - - +
77G GLU* 1.3 56.6 + - - +
78G ILE 3.3 0.2 - - - -
79G ILE* 3.7 13.0 - - + -
80G LEU* 2.9 26.0 + - - +
572I ILE* 4.3 27.1 - - + +
628I TYR* 3.2 16.8 - - + +
703I ILE* 5.7 1.8 - - + -
830I LYS* 4.9 11.7 - - + +
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Residues in contact with GLU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G GLU* 3.5 30.7 - - + +
74G ASP* 3.0 33.3 + - - +
75G VAL 3.1 0.2 - - - -
76G VAL* 1.3 78.7 - - - +
78G ILE* 1.3 51.8 + - - +
80G LEU* 3.2 31.2 - - - +
81G ASN* 2.7 34.7 + - - +
572I ILE* 5.4 4.9 - - - +
640I ARG* 3.5 32.8 + - - +
642I ARG* 5.2 3.2 + - - -
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Residues in contact with ILE 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G ILE* 4.8 13.2 - - + -
71G VAL* 4.1 6.3 - - + -
73G GLU* 3.6 23.6 - - + +
74G ASP 3.0 17.7 + - - +
75G VAL* 2.9 9.9 + - - +
77G GLU* 1.3 74.3 - - - +
79G ILE* 1.3 56.7 + - + +
80G LEU 3.1 1.6 - - - -
81G ASN* 2.8 30.3 + - - +
82G LEU* 2.9 23.8 + - + +
129G ILE* 3.6 29.3 - - + +
130G ALA* 3.7 21.1 - - + -
138G LEU* 5.3 2.7 - - + -
140G MET* 4.5 13.7 - - + -
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Residues in contact with ILE 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G VAL* 5.2 3.8 - - + -
64G GLU* 3.3 39.7 - - + +
75G VAL* 2.9 31.2 + - + +
76G VAL* 3.7 13.0 - - + +
78G ILE* 1.3 73.4 - - + +
80G LEU* 1.3 67.4 + - - +
82G LEU* 3.0 35.3 + - + +
83G LYS* 3.5 16.6 + - + +
165G ILE* 4.1 13.0 - - + -
167G VAL* 3.6 32.5 - - + -
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G VAL 2.9 15.3 + - - +
77G GLU* 3.2 38.1 - - - +
79G ILE* 1.3 78.2 - - - +
81G ASN* 1.3 66.1 + - - +
82G LEU 3.7 0.2 + - - -
83G LYS* 4.4 8.6 + - - +
84G GLU* 3.2 26.0 + - + +
573I ARG* 3.5 51.4 - - + +
697I ARG 5.0 2.0 - - - +
698I ASP* 5.2 11.2 - - + +
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Residues in contact with ASN 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G GLU* 5.3 2.2 - - - +
77G GLU* 2.7 37.1 + - - +
78G ILE* 2.8 17.0 + - - +
80G LEU* 1.3 84.9 - - - +
82G LEU* 1.3 63.1 + - - +
83G LYS 3.5 0.7 - - - -
84G GLU* 3.6 11.9 + - + +
85G LEU* 4.4 0.3 - - - +
127G LEU* 3.3 32.0 - - + +
128G HIS 3.6 22.3 - - - +
129G ILE* 3.9 16.3 + - - +
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G VAL* 4.2 20.1 - - + +
56G VAL* 3.6 33.0 - - + -
78G ILE* 2.9 22.1 + - + +
79G ILE* 3.0 35.5 + - + +
81G ASN* 1.3 74.9 - - - +
83G LYS* 1.3 63.1 + - + +
84G GLU 3.1 4.7 - - - -
85G LEU* 3.4 24.2 + - + +
114G PHE* 4.7 6.1 - - + -
129G ILE* 4.5 16.4 - - + -
140G MET* 4.3 20.0 - - + -
142G VAL* 4.7 11.4 - - + -
167G VAL* 5.7 0.7 - - + -
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Residues in contact with LYS 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G ALA* 3.5 29.1 - - + +
53G VAL* 4.5 4.5 - - + -
79G ILE* 3.5 22.7 + - + +
80G LEU* 4.4 5.7 + - - +
82G LEU* 1.3 72.4 - - + +
84G GLU* 1.3 67.5 + - - +
85G LEU 3.1 9.6 + - - +
167G VAL* 3.6 22.4 - - + -
168G ASP* 3.1 56.5 + - - +
170G ILE* 4.5 20.8 - - + +
696I LYS 4.0 5.0 + - - -
698I ASP* 2.6 30.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il